GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PPDCalpha in Sinorhizobium meliloti 1021

Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate SMc03201 SMc03201 2-oxoisovalerate dehydrogenase subunit alpha

Query= BRENDA::A0A222AKA3
         (368 letters)



>FitnessBrowser__Smeli:SMc03201
          Length = 410

 Score =  180 bits (457), Expect = 5e-50
 Identities = 119/342 (34%), Positives = 171/342 (50%), Gaps = 23/342 (6%)

Query: 35  AGVPPDRQLLM-YRAMVVGRAFNRQATAFSRQGRLAVYPSSRGQEACQVGSALAVRPTDW 93
           AG   D +LL   R M++ RAF+ +     RQG+ + Y    G+EA       A+R  D 
Sbjct: 69  AGFLSDEELLTGLRHMMLLRAFDARMLMAQRQGKTSFYMQHLGEEAVSCAFRKALRKGDM 128

Query: 94  LFPTYRESVALLTRGIDPVQVLTLFRGDQHCGYDPVTEHTAPQCTP------------LA 141
            FPTYR++  L+      V+++     ++    DP      P                LA
Sbjct: 129 NFPTYRQAGLLIADDYPMVEMMNQIFSNE---LDPCHGRQLPVMYTSKEHGFFTISGNLA 185

Query: 142 TQCLHAAGLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLVQNNQYA 201
           TQ + A G A A+ +  D  +A  +IGDG+T+E DFH AL +A+  +APV+  + NNQ+A
Sbjct: 186 TQYVQAVGWAMASAIKNDTRIAAGWIGDGSTAESDFHSALVFASTYKAPVILNIVNNQWA 245

Query: 202 ISVPLA-KQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPTLIEAV 260
           IS      +  + T A +  G+G+P +R+DGND L VY     AAERAR   GPTLIE V
Sbjct: 246 ISTFQGIARGGSGTFAARGLGFGIPALRVDGNDYLAVYAVARWAAERARLNLGPTLIEYV 305

Query: 261 TYRIDAHTNADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGV-LDRAAADGIAAAADAF 319
           TYR+ AH+ +DD + YRP  E++ W   DPV RL++ L+  G   +   A   A   D  
Sbjct: 306 TYRVGAHSTSDDPSAYRPKTESEAWPLGDPVLRLKKHLILRGAWSEERHAQAEAEIMDEV 365

Query: 320 -----AGELSARFSAPPTGDPMQMFRHVYHHLPPHLREQSER 356
                  E      A        +F  VY  +PPH+R Q ++
Sbjct: 366 IQAQKEAERHGTLHAGGRPSVRDIFEGVYAEMPPHIRRQRQK 407


Lambda     K      H
   0.319    0.132    0.395 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 333
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 368
Length of database: 410
Length adjustment: 30
Effective length of query: 338
Effective length of database: 380
Effective search space:   128440
Effective search space used:   128440
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory